I've had to help a few people with weird quirks between SAI and Wacom Tablets. Specifically with Cintiqs. I figured it would be good to list a few of the weird quirks I've found and their work-arounds somewhere, so I'm going to paste them here.
I find the line smoothing features worth some of the weirdness SAI has, even if I have to pull it into Photoshop later to add text or change things. 'Drawing' in SAI is really, really fluid and natural. I can't NOT use it now.
I have a Cintiq 12WX (the smaller one) and a second monitor. I'm going to assume you have a second monitor as well. If not, just skip that section.
Multi-Monitors:
http://sad